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Related Concept Videos

Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Protein-Protein Interfaces02:04

Protein-Protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...

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Related Experiment Video

Updated: Jul 4, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

Coevolution at protein complex interfaces can be detected by the complementarity trace with important impact for

Hocine Madaoui1, Raphaël Guerois

  • 1Commissariat à l'Energie Atomique (CEA), Institut de Biologie et Technologies de Saclay, and Centre National de la Recherche Scientifique (CNRS), Gif-sur-Yvette, F-91191, France.

Proceedings of the National Academy of Sciences of the United States of America
|May 31, 2008
PubMed
Summary

We developed the Surface COmplementarity Trace in Complex History (SCOTCH) score to predict protein-protein complex structures. SCOTCH effectively identifies correct structures by assuming mutations minimally disrupt residue interactions during evolution.

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Area of Science:

  • Structural biology
  • Evolutionary biology
  • Biophysics

Background:

  • Protein-protein interactions are crucial for biological processes and are under evolutionary selection.
  • Predicting the structure of macromolecular assemblies is essential for understanding their function.
  • Understanding evolutionary constraints on protein interfaces is key to improving structure prediction.

Purpose of the Study:

  • To develop a novel scoring method for predicting protein-protein complex structures.
  • To leverage evolutionary principles, specifically the conservation of physicochemical compatibility at interfaces.
  • To assess the performance of the new method against existing approaches.

Main Methods:

  • Development of the Surface COmplementarity Trace in Complex History (SCOTCH) score.
  • Assumption that evolutionary mutations minimally disrupt interface residue compatibility.
  • Validation on 129 known protein-protein complexes with permanent and transient interactions.

Main Results:

  • The SCOTCH score demonstrated high efficiency in discriminating correct protein-protein complex structures.
  • SCOTCH outperformed other evolution-based methods (conservation, coevolution) and statistical scoring methods.
  • The method was validated on a diverse set of complexes.

Conclusions:

  • SCOTCH is a robust strategy for guiding the prediction of protein-protein complex structures.
  • The approach provides a framework for tracking the evolution of protein surfaces while maintaining interactions.
  • This work advances the field of structural prediction and evolutionary analysis of protein complexes.